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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-07 12:03:40 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-07 14:55:21 +0100
commit7035cde3a53781721fe15a8893fdf328c789bdd2 (patch)
treea1e4929faf9d645caedc0ed4dcc5036252497c63 /README.md
parent77c248ca40b82ec00a756cd82f12968131f78959 (diff)
Remove nlmixr interface for release of mkin 1.1.0
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
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@@ -96,9 +96,16 @@ version is found in the ['dev' subdirectory](https://pkgdown.jrwb.de/mkin/dev/).
interpretation of the model parameters.
* Nonlinear mixed-effects models can be created from fits of the same degradation
model to different datasets for the same compound by using the
- [nlme.mmkin](https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html) method.
- Note that the convergence of the nlme fits depends on the quality of the data.
- Convergence is better for simple models and data for many groups (e.g. soils).
+ [nlme.mmkin](https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html) and
+ [saem.mmkin](https://pkgdown.jrwb.de/mkin/reference/saem.mmkin.html) and
+ methods. Note that the convergence of the nlme fits depends on the quality of
+ the data. Convergence is better for simple models and data for many groups
+ (e.g. soils). The saem method uses the `saemix` package as a backend. Analytical
+ solutions suitable for use with this package have been implemented for parent
+ only models and the most important models including one metabolite (SFO-SFO
+ and DFOP-SFO). Fitting other models with `saem.mmkin`, while it makes use
+ of the compiled ODE models that mkin provides, has longer run times (at least
+ six minutes on my system).
### Performance

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